After accusations of sexual harassment and physical and verbal abuse, Peter Martins, the powerful leader of New York City Ballet who shaped the company for more than three decades, has decided to retire.

“I have denied, and continue to deny, that I have engaged in any such misconduct,” Mr. Martins, 71, wrote in a letter dated on Monday informing the board of his retirement, which takes effect immediately.

Mr. Martins, who has been on leave as the company investigates his actions, added, “I cooperated fully in the investigation and understand it will be completed shortly. I believe its findings would have vindicated me.”

Charles W. Scharf, the chairman of City Ballet’s board, issued a statement on Monday thanking Mr. Martins for his contributions, but noted the investigation will continue: “The board takes seriously the allegations that have been made against him and we expect the independent investigation of those allegations to be completed soon.”

Board members were told of his decision in a conference call Monday evening, when they also learned that he had been arrested on Thursday and charged with driving while intoxicated in Westchester County, according to a person with knowledge of the meeting who requested anonymity because the discussions were confidential.

Mr. Martins was charged in Ardsley, N.Y., after a minor accident in the village square, the police chief, Emil J. Califano, said by telephone Monday night. In a previous incident, in 2011, he pleaded guilty to driving while intoxicated.

In his letter, Mr. Martins said the abuse and harassment accusations by dancers had “exacted a painful toll on me and my family.” He said he had decided to retire to “bring an end to this disruption.”

Mr. Scharf said in his statement that the company and its School of American Ballet “will convene a committee promptly to begin the search for a new ballet master in chief.” Last month it appointed an interim four-person team to lead the company.

Five City Ballet dancers — one of whom is still with the company — recently came forward in The New York Times to describe verbal and physical abuse dating as far back as 1993.

His departure could create more turmoil within the company. As the investigation was being conducted, an apparent split emerged among former and current dancers over the fate of Mr. Martins.

In recent interviews, 24 women and men — all former dancers at the company or its school — described a culture of intimidation under Mr. Martins, which they said has hurt the careers of generations of performers.

The former dancers said that when they worked under Mr. Martins, they and many peers had been too afraid to complain as he verbally and physically bullied performers and students; shamed them about their bodies; and abused his power by conducting sexual relationships with select dancers.

Vanessa Carlton, a former dancer with the school, recently sent an email to Robert I. Lipp, a vice chairman of City Ballet.

“Dancers tend not to talk,” wrote Ms. Carlton, now a singer-songwriter. “I’m concerned that this reticence is being misread as a sign to you and your fellow board members that they are not upset.”

She continued, “Every single ex-dancer that I know, including myself, will be devastated if Peter is allowed to waltz back into his office.”

In the other camp were several current dancers who, before Mr. Martins’s resignation, said the accusations against him did not jibe with the leader they know and that the complaints were coming from dancers who had left the company.

“He has been nothing but respectful of me,” Sterling Hyltin, a longtime principal ballerina, said in a recent interview. “It’s been really upsetting to see former dancers speaking on behalf of current dancers.”

Among current dancers in the ballet, several defended Mr. Martins. Megan Fairchild and a fellow dancer, Megan Johnson, reached out to The New York Times on their own to say he has always behaved professionally with them.

“I’ve never felt in danger in his presence,” said Ms. Fairchild, who has been with the company for 16 years. “He’s the person I go to when I’m having trouble in the company or in life.”

City Ballet is not the only challenging company in which to pursue a career. Many in the dance world have expressed hope over the last several weeks that these revelations will prompt overdue changes to a culture in which bullying, body-shaming and sexual favors have long been part of the business.

“It can feel particularly risky — both emotionally and career wise — to be a whistle-blower within our field,” Wendy Whelan, a 30-year star dancer with the company who retired in 2014, said. “We aren’t encouraged to use our voice to expose the dark side of what is also truly a magical industry for the sake of hurting our father-figure teachers.”

“The tradition of balletic patriarchy has held a closet full of skeletons,” she added. “In recent light of things, many artists and dancers are seeing that society is no longer accepting these kind of behaviors as normal, so why do we?”

Several former ballet dancers said in the recent interviews that Mr. Martins was known for having intimate relationships with dancers, some of whom seemed to receive better roles. The relationships were complicated by a power dynamic, they said, in which Mr. Martins was widely viewed as a near deity, particularly to young dancers who might go to any length — from starving themselves to having sex with him — to earn his praise and attention.

City Ballet leaders, before the announcement, said the lawyer heading their investigation, Barbara Hoey, was engaged “in a good-faith effort to investigate recent allegations against Peter Martins”; that the company “prohibits retaliation” against participants; and that it encourages “anyone with relevant information to come forward.”

Beyond its legendary founder, George Balanchine, there is no one who has done more to shape the company than Peter Martins. His history with City Ballet dates to 1967, when he was invited to dance the title role in Balanchine’s “Apollo” at the Edinburgh Festival. He became a principal dancer in 1970, widely acclaimed for his expert partnering and masculine grace.

After the death of Balanchine in 1983, Mr. Martins took over leadership of the company with Jerome Robbins; in 1989, he became the sole ballet master in chief. Mr. Martins has also served as the artistic director and chairman of the school’s faculty.

Throughout his tenure, Mr. Martins has had his share of supporters and detractors. Some credit him for balancing the company’s loyalty to Balanchine with the commissioning of new choreography, particularly the opportunities he provided to promising young choreographers like Alexei Ratmansky, Christopher Wheeldon and Justin Peck.

Mr. Peck is considered a candidate to succeed Mr. Martins, as is Ms. Whelan and the French choreographer Benjamin Millepied.

Some critics have questioned Mr. Martins’s views of women based on his choreography. In reviewing “T-al-a Gaisma,” in 2005 — which featured Miranda Weese, Jock Soto and Mr. Martins’s wife, Darci Kistler — Joan Acocella in The New Yorker alluded to “what seems to be his mixed feelings about women.”

“Weese is made into a succubus, Kistler into a pleading pest, hanging on to Soto, getting her hair tangled up in his hands,” she wrote. “Soto finally fights his way free, lowering these harridans onto the floor, where they lie supine, immobilized.”

Mr. Martins has been subject to public scrutiny for his conduct in the past. In 1992, he was arrested on charges of assaulting Ms. Kistler; she later dropped the charges.

Al Baker contributed reporting.

A version of this article appears in print on , on Page A1 of the New York edition with the headline: City Ballet Leader Retires Amid Abuse Claims. Order Reprints | Today’s Paper | Subscribe